[petsc-users] Valgrind Issue With Ghosted Vectors

[Zhang, Junchao]

Yes, it does.  It is a bug.
--Junchao Zhang


On Thu, Mar 21, 2019 at 11:16 AM Balay, Satish <balay at mcs.anl.gov<mailto:balay at mcs.anl.gov>> wrote:
Does maint also need this fix?

Satish

On Thu, 21 Mar 2019, Stefano Zampini via petsc-users wrote:

> Derek
>
> I have fixed the optimized plan few weeks ago
>
> https://bitbucket.org/petsc/petsc/commits/c3caad8634d376283f7053f3b388606b45b3122c
>
> Maybe this will fix your problem too?
>
> Stefano
>
>
> Il Gio 21 Mar 2019, 04:21 Zhang, Junchao via petsc-users <
> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> ha scritto:
>
> > Hi, Derek,
> >   Try to apply this tiny (but dirty) patch on your version of PETSc to
> > disable the VecScatterMemcpyPlan optimization to see if it helps.
> >   Thanks.
> > --Junchao Zhang
> >
> > On Wed, Mar 20, 2019 at 6:33 PM Junchao Zhang <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>> wrote:
> >
> >> Did you see the warning with small scale runs?  Is it possible to provide
> >> a test code?
> >> You mentioned "changing PETSc now would be pretty painful". Is it because
> >> it will affect your performance (but not your code)?  If yes, could you try
> >> PETSc master and run you code with or without -vecscatter_type sf.  I want
> >> to isolate the problem and see if it is due to possible bugs in VecScatter.
> >> If the above suggestion is not feasible, I will disable VecScatterMemcpy.
> >> It is an optimization I added. Sorry I did not have an option to turn off
> >> it because I thought it was always useful:)  I will provide you a patch
> >> later to disable it. With that you can run again to isolate possible bugs
> >> in VecScatterMemcpy.
> >> Thanks.
> >> --Junchao Zhang
> >>
> >>
> >> On Wed, Mar 20, 2019 at 5:40 PM Derek Gaston via petsc-users <
> >> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
> >>
> >>> Trying to track down some memory corruption I'm seeing on larger scale
> >>> runs (3.5B+ unknowns).  Was able to run Valgrind on it... and I'm seeing
> >>> quite a lot of uninitialized value errors coming from ghost updating.  Here
> >>> are some of the traces:
> >>>
> >>> ==87695== Conditional jump or move depends on uninitialised value(s)
> >>> ==87695==    at 0x73236D3: PetscMallocAlign (mal.c:28)
> >>> ==87695==    by 0x7323C70: PetscMallocA (mal.c:390)
> >>> ==87695==    by 0x739048E: VecScatterMemcpyPlanCreate_Index (vscat.c:284)
> >>> ==87695==    by 0x73A5D97: VecScatterMemcpyPlanCreate_PtoP
> >>> (vpscat_mpi1.c:312)
> >>> ==64730==    by 0x7393E8A: VecScatterSetUp_vectype_private (vscat.c:857)
> >>> ==64730==    by 0x7395E5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)
> >>> ==64730==    by 0x73DDD39: VecScatterSetUp (vscatfce.c:212)
> >>> ==64730==    by 0x73DCD73: VecScatterCreateWithData (vscreate.c:333)
> >>> ==64730==    by 0x7444232: VecCreateGhostWithArray (pbvec.c:685)
> >>> ==64730==    by 0x744490D: VecCreateGhost (pbvec.c:741)
> >>>
> >>> ==133582== Conditional jump or move depends on uninitialised value(s)
> >>> ==133582==    at 0x4030384: memcpy@@GLIBC_2.14
> >>> (vg_replace_strmem.c:1034)
> >>> ==133582==    by 0x739E4F9: PetscMemcpy (petscsys.h:1649)
> >>> ==133582==    by 0x739E4F9: VecScatterMemcpyPlanExecute_Pack
> >>> (vecscatterimpl.h:150)
> >>> ==133582==    by 0x739E4F9: VecScatterBeginMPI1_1 (vpscat_mpi1.h:69)
> >>> ==133582==    by 0x73DD964: VecScatterBegin (vscatfce.c:110)
> >>> ==133582==    by 0x744E195: VecGhostUpdateBegin (commonmpvec.c:225)
> >>>
> >>> This is from a Git checkout of PETSc... the hash I branched from is:
> >>> 0e667e8fea4aa from December 23rd (updating would be really hard at this
> >>> point as I've completed 90% of my dissertation with this version... and
> >>> changing PETSc now would be pretty painful!).
> >>>
> >>> Any ideas?  Is it possible it's in my code?  Is it possible that there
> >>> are later PETSc commits that already fix this?
> >>>
> >>> Thanks for any help,
> >>> Derek
> >>>
> >>>
>

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